Our current understanding of autism spectrum disorders (ASD) delineates a highly heritable, yet etiologically heterogeneous disease. Forward genetic approaches to find disease associated mutations or common variation have been successful and continue to offer considerable power. Yet, given the accumulating evidence for very significant heterogeneity and environmental influences, complementary approaches to classic forward genetics become necessary. Genetic polymorphism and mutation data to date have identified dozens of causal or contributory variants, yet our preliminary data from autism brain suggest that common molecular pathways are involved in a significant subset of cases. This convergence at the tissue level suggests that other mechanisms, specifically epigenetic changes, combined with genetic background, are contributing to such final common pathways. We propose to further test this hypothesis by taking a comprehensive and integrative genome-wide approach to assessing brain gene-expression, miRNA levels and the related, causal epigenetic mechanisms in ASD etiology. The work proposed here, which brings together three principal investigators with a publication track record and clear expertise in all of the methods and approaches necessary, comprises a unique international collaborative group capable of performing this work using state of the art techniques. We will perform RNA-seq analyses of four cerebral cortical regions and cerebellum from ASD cases and controls, to assess mRNA, miRNA, and splicing isoform regulation. In parallel, we will identify key differences in chromatin state and DNA methylation across multiple brain regions in the same ASD and control individuals used in the expression analyses using ChIP-Seq and MeDIP . We will thus assess the mechanisms by which changes in DNA methylation, histone modification, and DNA sequence contribute to the observed differences in gene expression, and we will explore the hypothesis that epigenetic processes mediate susceptibility for ASD via long-term changes in transcriptional regulation. This work, which represents an unprecedented effort to unify these often disparate data (usually produced without integration in mind), will delineate potential shared molecular pathways in ASD and the underlying mechanism of these differences at the level of miRNA, the chromatin regulatory apparatus, and DNA methylation. In addition, these data will be made available to the community in a web-based format to be of maximum utility.